During the summer, Harry is frustrated by the lack of communication from his friends and by Dumbledore's refusal to let him help in the struggle against Lord Voldemort. One evening, Dementors attack him and his cousin Dudley, but Harry fends them off using the Patronus Charm. Later, members of the Order of the Phoenix arrive at the Dursley residence and take Harry to Number 12, Grimmauld Place. Number 12 is Sirius Black's family home and the headquarters of the Order, which is a secret organisation founded by Dumbledore to fight Voldemort and his Death Eaters. Harry wants to join the Order, but is too young.

Under the leadership of Cornelius Fudge, the Ministry of Magic is waging a smear campaign against Harry and Dumbledore, claiming they are lying about the return of Voldemort. Harry faces legal charges for the Patronus Charm he performed, but is exonerated and returns to Hogwarts. Dolores Umbridge, a senior Ministry employee, is the new Defence Against the Dark Arts professor. She implements a textbook-only curriculum and forbids the students from practising defensive spells. Harry, Ron, and Hermione form a secret student group called Dumbledore's Army, which meets in the Room of Requirement to practice defensive magic under Harry's instruction.

One night, Harry dreams that Arthur Weasley is attacked by Voldemort's snake, Nagini. The attack actually occurred, and Dumbledore realises that Harry's mind is connected to Voldemort. He orders Professor Snape to teach Harry Occlumency to keep Voldemort out of his mind. When Umbridge discovers Dumbledore's Army, Dumbledore saves Harry from expulsion by claiming he formed the group. Dumbledore then goes into hiding to avoid arrest. Umbridge is appointed headmistress and begins enacting strict rules and regulations.

During exams, Harry has a vision of Voldemort torturing Sirius at the Department of Mysteries. He attempts to contact Sirius at Grimmauld Place, but Umbridge catches and interrogates him, admitting she sent the Dementors. Hermione intervenes and convinces Umbridge to go with her and Harry into the Forbidden Forest. When Umbridge provokes the centaurs who live there, they take her captive. Harry and his friends fly to the Ministry to rescue Sirius, but he is not there. Instead, they find shelves containing glass spheres, one of which bears Harry's name. Harry picks it up and is immediately surrounded by Death Eaters. Lucius Malfoy reveals that Harry was lured to the Ministry by a false vision from Voldemort, who wishes to hear the prophecy contained in the sphere. He asks Harry for the sphere, but Harry refuses to give it to him.

The students fight the Death Eaters with help from several Order of the Phoenix members. Neville accidentally knocks the sphere down some steps, destroying it. Bellatrix Lestrange attacks Sirius, and he disappears through a mysterious stone archway to his death. Voldemort appears and tries to kill Harry, but Dumbledore arrives and thwarts him. Fudge and other Ministry of Magic employees arrive on the scene and witness Voldemort just before he flees. Back at Hogwarts, Dumbledore tells Harry the prophecy was made by Professor Trelawney, who predicted the birth of a child with the power to vanquish Voldemort. This prophecy caused Voldemort to murder Harry's parents, and it is why he wishes to kill Harry as well. Harry feels overwhelmed by the prophecy and the loss of his godfather, but the wizarding community now believes him and respects him. Motivated by his friends, Harry returns to the Dursleys for the summer.